rs29646780 SNP Detail

Summary

• ID
  rs29646780
• Variation Type
  SNP
• Alleles
  C/T

• Created in dbSNP Build
  125
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr3:28319010 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TCCCATTGCA GCCTCGACGC
  TTCCCCACCC CCACCTCTAA TCCCAGCACA CTCCTTCGGG GAAGGGGGCC GAGCGCTCTT
  GCCATTTTAA TTAGATGCTG CCTGCCAGGA AGGGGGTGAG GAGGGGTGGT GGCCTTGGCA
  GCAGCAGGCA TCTGAGAAAG ATTGGACACC AATCTCAGTT CCACTAGTTT CTTCCTCTCC
  Y
  GAACTAAAAA TAAAATAAAC AGCAAATGCA TATGCTTGAT GCCTGGAGGG TAGGTGAGAC
  CTAAGAGATG GTGTCTCATC TCATGTCACC CACCGCCAGT AGGGGTGGAA GTTCAGTGGT
  TCTCCGGAAC ACATTGTTAG ATTGATGCTA GAATCTTGAG GCCGTTTACC TGTGTCTACT
  AAAGCCTTCC TGCCCTTACA                                            
  
  Y = C/T
  

  
  Note: Sequence in lower case indicates low-complexity or repetitive sequence

  ---

SNP Assays
and
SNP Consensus

Strain alleles of submitted assays, and consensus values for this SNP

Assay ID	Submitter SNP ID	Submitter Handle	Population	ss orientation	Variation Type	129S1/SvImJ	A/J	AKR/J	BALB/cByJ	BTBR T<+> Itpr3/J	C3H/HeJ	CAST/EiJ	DBA/2J	FVB/NJ	KK/HlJ	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
ss46866519	NES10823061	PERLEGEN	MM_PANEL2	f	SNP	C	C	C	C	C	C	C	C	C	C	T	C	C	T	C
SNP Consensus Information
SNP					Consensus Type	129S1/SvImJ	A/J	AKR/J	BALB/cByJ	BTBR T<+> Itpr3/J	C3H/HeJ	CAST/EiJ	DBA/2J	FVB/NJ	KK/HlJ	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
rs29646780					SNP	C	C	C	C	C	C	C	C	C	C	T	C	C	T	C

Additional submitted assays for this SNP, where the strain of origin for observed alleles is not specified by the submitter

Assay ID	Submitter SNP ID	Submitter Handle	Population	ss orientation	Variation Type	Alleles
ss46866519	NES10823061	PERLEGEN	MM_PANEL	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:28319010 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi13025	CpG island 13025			838 bp distal
Gm54170	predicted gene, 54170			within coordinates
Gm56802	predicted gene, 56802			within coordinates
Rr574555	regulatory region 574555			1208 bp distal
Rr574556	regulatory region 574556			657 bp distal
Rr574557	regulatory region 574557			within coordinates
Rr574558	regulatory region 574558			367 bp proximal
Tnik	TRAF2 and NCK interacting kinase			Intron
				Noncoding-Transcript-Variant
Tssr28643	transcription start site region 28643			1647 bp downstream
Tssr28644	transcription start site region 28644			1528 bp downstream
Tssr28645	transcription start site region 28645			1475 bp downstream
Tssr28646	transcription start site region 28646			1448 bp downstream
Tssr28647	transcription start site region 28647			1433 bp downstream
Tssr28648	transcription start site region 28648			1424 bp downstream
Tssr28649	transcription start site region 28649			1284 bp downstream
Tssr32865	transcription start site region 32865			612 bp upstream
Tssr32866	transcription start site region 32866			369 bp downstream